The Bill of Rights, when originally written, was not intended to apply to all men. Slaves, for example, were not entitled to any of these protections. The Amendments abolishing slavery and extending the BOR to the states does not contain language extending the BOR to those beyond the formal legal jurisdiction of the U.S.
Sometimes people say that we don't have to respect people's rights if they aren't Americans. I think that we should respect their rights because we are Americans.
A "right" is a legal rule applicable between two people within a framework of law. Foreigners don't have any "rights" as against the American people not because they're bad or we're more important or anything like that, but because they are not part of a common legal framework with us.
Unless you believe in a God, the concept of "natural rights" is utterly ridiculous. Lots of people believe in them, unfortunately, but then again at one point many very smart people believed there were four elements: earth, air, fire, and water.
I don't see that way. They are all value judgements. Earth, air, fire and water all exist and people can consider them primary if they want to. The same is true with rights. It depends upon what you value.
There is a difference between thinking that something is important and thinking that something expresses a deeper physical reality. That earth, wind, fire, and water are primary is a value judgment--that everything else is made of one of these four elements is a (false) factual assertion.
The same thing with natural rights. You might think it's important not to kill people, no matter if they're American or not. That's a value judgment. But to assert they have a "natural right" not to be killed--that's a factual assertion. If you do kill them and do an autopsy, you won't find any "natural right" in there.
I don't link the notion of a "natural right" to "expressing a deeper physical reality." That's your definition. In any case, I stand by what I said: respecting human life should be considered part of our values. It was a foundational idea at the start of our country.